Merge pull request #315 from EGA-archive/develop

genomicVariations get request parameter filters fixed

beacon/db/filters.py

@@ -411,8 +411,10 @@ def apply_ontology_filter(query: dict, filter: OntologyFilter, collection: str,
 
 
     scope = filter.scope
-    if scope is None:
+    if scope is None and collection != 'g_variants':
         scope = collection[0:-1]
+    elif scope is None:
+        scope = 'genomicVariation'
     LOG.debug(scope)
     is_filter_id_required = True
     # Search similar
@@ -653,8 +655,10 @@ def format_operator(operator: Operator) -> str:
 def apply_alphanumeric_filter(query: dict, filter: AlphanumericFilter, collection: str) -> dict:
     #LOG.debug(filter.value)
     scope = filter.scope
-    if scope is None:
+    if scope is None and collection != 'g_variants':
         scope = collection[0:-1]
+    elif scope is None:
+        scope = 'genomicVariation'
     formatted_value = format_value(filter.value)
     formatted_operator = format_operator(filter.operator)
     #LOG.debug(collection)
@@ -890,8 +894,10 @@ def apply_custom_filter(query: dict, filter: CustomFilter, collection:str) -> di
     #LOG.debug(query)
 
     scope = filter.scope
-    if scope is None:
+    if scope is None and collection != 'g_variants':
         scope = collection[0:-1]
+    elif scope is None:
+        scope = 'genomicVariation'
     value_splitted = filter.id.split(':')
     if value_splitted[0] in conf.alphanumeric_terms:
         query_term = value_splitted[0]

beacon/db/g_variants.py

@@ -207,11 +207,14 @@ def get_variants(entry_id: Optional[str], qparams: RequestParams, dataset: str):
     query_parameters, parameters_as_filters = apply_request_parameters({}, qparams)
     LOG.debug(query_parameters)
     LOG.debug(parameters_as_filters)
-    if parameters_as_filters == True:
+    if parameters_as_filters == True and query_parameters != {'$and': []}:
         query, parameters_as_filters = apply_request_parameters({}, qparams)
         query_parameters={}
-    else:
+    elif query_parameters != {'$and': []}:
         query=query_parameters
+    elif query_parameters == {'$and': []}:
+        query_parameters = {}
+        query={}
     query = apply_filters(query, qparams.query.filters, collection,query_parameters)
     LOG.debug(query)
     include = qparams.query.include_resultset_responses